Purification of oligonucleotides by high affinity, low molecular weight displacers

Sustainability Challenges and Opportunities in Oligonucleotide Manufacturing

With a renewed and growing interest in therapeutic oligonucleotides across the pharmaceutical industry, pressure is increasing on drug developers to take more seriously the sustainability ramifications of this modality. With 12 oligonucleotide drugs reaching the market to date and hundreds more in clinical trials and preclinical development, the current state of the art in oligonucleotide production poses a waste and cost burden to manufacturers. Legacy technologies make use of large volumes of hazardous reagents and solvents, as well as energy-intensive processes in synthesis, purification, and isolation. In 2016, the American Chemical Society (ACS) Green Chemistry Institute Pharmaceutical Roundtable (GCIPR) identified the development of greener processes for oligonucleotide Active Pharmaceutical Ingredients (APIs) as a critical unmet need. As a result, the Roundtable formed a focus team with the remit of identifying green chemistry and engineering improvements that would make oligonucleotide production more sustainable. In this Perspective, we summarize the present challenges in oligonucleotide synthesis, purification, and isolation; highlight potential solutions; and encourage synergies between academia; contract research, development and manufacturing organizations; and the pharmaceutical industry. A critical part of our assessment includes Process Mass Intensity (PMI) data from multiple companies to provide preliminary baseline metrics for current oligonucleotide manufacturing processes.

Detection of trace proteins in multicomponent mixtures using displacement chromatography

Model protein feed mixtures containing three abundant and seven trace proteins at various concentrations were identified and employed in a series of displacement experiments. Reversed-phase liquid chromatography (RPLC) and matrix assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry were used to evaluate the compositions of both the feed mixtures and effluent fractions from the displacement experiments. The results demonstrated that trace proteins were focused at the boundaries between the abundant solutes where they were enriched and concentrated. For many of the multicomponent feed mixtures, mass spectrometry analyses of the displacement column effluent fractions resulted in the identification of trace proteins that were not detectable in the feed. In addition, the use of minimal or no salt in the carrier solutions enabled the analysis of displacement fractions by direct infusion mass spectrometry. These results are significant in that they indicate that while the presence of abundant proteins can often be problematic for the detection of trace components, displacement chromatography may be able to employ these abundant proteins to focus trace proteins in the displacement train, thus facilitating detection.

Synthesis and characterization of fluorescent displacers for online monitoring of displacement chromatography

One of the major impediments to the implementation of displacement chromatography for the purification of biomolecules is the need to collect fractions from the column effluent for time-consuming offline analysis. The ability to employ direct online monitoring of displacement chromatography would have significant implications for applications ranging from analytical to preparative bioseparations. To this end, a set of novel fluorescent displacers were rationally designed using known chemically selective displacers as a template. Fluorescent cores were functionalized with different charge moieties, creating a homologous library of displacers. These compounds were then tested on two protein pairs, alpha-chymotrypsinogen A/ribonuclease A and cytochrome c/lysozyme, using batch and column displacement experiments. Of the synthesized displacers, two were found to be highly selective while one was determined to be a high-affinity displacer. Column displacements using one of the selective displacers yielded complete separation of both protein pairs while facilitating direct online detection using UV and fluorescence detection. Saturation transfer difference NMR was also carried out to investigate the binding of the fluorescent displacers to proteins. The results indicated a selective binding between the selective displacers and alpha-chymotrypsinogen A, while no binding was observed for ribonuclease A, confirming that protein-displacer binding is responsible for the selectivity in these systems. This work demonstrates the utility of fluorescent displacers to enable online monitoring of displacer breakthroughs while also acting as efficient displacers for protein purification.

Multidimensional High-Throughput Screening of Displacers

A multidimensional, batch high-throughput screening (MD-HTS) protocol was developed to investigate the effects of various parameters on the selectivity of ion-exchange protein displacement systems. A variety of molecules were screened, and the results were employed to provided insights into the influence of displacer chemistry and concentration, resin chemistry, and mobile-phase salt counterion on the efficacy and selectivity of these nonlinear chromatographic systems. These results open up the possibility of tailoring the selectivity of displacement separations by choosing appropriate combinations of operating conditions using the MD-HTS technique. The screens were also employed for the identification of displacers and conditions for the separation of a challenging protein mixture by selective displacement chromatography. Column displacements were carried out with potential lead compounds identified from the MD-HTS screens, and the results confirmed that selective displacement could indeed be achieved for this model mixture. Furthermore, the results indicated that this approach is particularly useful when the order of elution is not changed, but the inherent selectivity is increased in the presence of the displacer. The results presented in this paper demonstrate the utility of the MD-HTS technique for rapid method development in protein ion-exchange displacement chromatography.

Adsorption of charged macromolecules on oppositely charged porous column materials

A family of cationic polyelectrolytes possessing defined chain lengths, narrow chain length distributions, uniform charge density, but substituents of different hydrophilicity at the quaternary ammonium group served as model compounds for adsorption studies. These studies quantitatively revealed that polymer characteristics and electrostatic parameters affect the adsorption behavior on oppositely charged porous column materials. The presence of electrostatic exclusion, in addition to size exclusion, was proved comparing molecular, electrostatic and geometrical parameters. The dominance of electrostatic effects could be concluded evaluating the relation between molecular and electrostatic dimensions. The results provide a contribution how to estimate the threshold for electrostatic exclusion from pores as a function of dimensions and experimental conditions.

Evaluation of selectivity changes in HIC systems using a preferential interaction based analysis

It is well established that salt enhances the interaction between solutes (e.g., proteins, displacers) and the weak hydrophobic ligands in hydrophobic interaction chromatography (HIC) and that various salts (e.g., kosmotropes, chaotropes, and neutral) have different effects on protein retention. In this article, the solute affinity in kosmotropic, chaotropic, and neutral mobile phases are compared and the selectivity of solutes in the presence of these salts is examined. Since solute binding in HIC systems is driven by the release of water molecules, the total number of released water molecules in the presence of various types of salts was calculated using the preferential interaction theory. Chromatographic retention times and selectivity reversals of both proteins and displacers were found to be consistent with the total number of released water molecules. Finally, the solute surface hydrophobicity was also found to have a significant effect on its retention in HIC systems.

Application of hydrophobic interaction displacement chromatography for an industrial protein purification

Recently it has been established that low molecular weight displacers can be successfully employed for the purification of proteins in hydrophobic interaction chromatography (HIC) systems. This work investigates the utility of this technique for the purification of an industrial protein mixture. The study involved the separation of a mixture of three protein forms, that differed in the C-terminus, from their aggregate impurities while maintaining the same relative ratio of the three protein forms as in the feed. A batch high-throughput screening (HTS) technique was employed in concert with fluorescence spectroscopy for displacer screening in these HIC systems. This methodology was demonstrated to be an effective tool for identifying lead displacer candidates for a particular protein/stationary-phase system. In addition, these results indicate that surfactants can be employed at concentrations above their CMCs as effective displacers. Displacement of the recombinant proteins with PEG-3400 and the surfactant Big Chap was shown to increase the productivity as compared to the existing step-gradient elution process.

Comparison of preparative characteristics of micro open parallel plate separators and microbore columns for concentration of trace species by displacement chromatography

The potential for preparative concentration of trace species by displacement chromatography in a micro open parallel plate separator (microOPPS) has been explored. A comparison of the performance of the microOPPS with micro open tubular columns (microOTC) has been presented. Using simulation models, the effects of operating and equilibrium parameters on throughput and yield have been determined. It is shown that the microOPPS can offer considerable advantages over the traditional microOTCs. Most significantly, throughputs can be enhanced by more than an order of magnitude in many cases. This is primarily due to the higher loading per cycle in the microOPPS, made possible by the ability to change the depth of the channel independent of the width. While yield is generally lower in the microOPPS, this effect can be overcome by the proper selection of operating conditions.

Purification of an oligonucleotide at high column loading by high affinity, low-molecular-mass displacers

The development of efficient techniques for large-scale oligonucleotide purification is of great interest due to the increased demand for antisense oligonucleotides as therapeutics as well as their use for target validation and gene functionalization. This paper describes the use of anion-exchange displacement chromatography for the purification of 20-mer phosphorothioate oligonucleotide from its closely related impurities using low-molecular-mass amaranth as the displacer. Experiments were carried out to examine the effect of the feed load on the performance of the displacement chromatography. In contrast to prior work, displacement chromatography was successfully scaled-up to high column loadings while maintaining high purity and yields. Experiments carried out on a Source 15Q column indicated that crude oligonucleotide loading as high as 39.2 mg/ml of column were readily processed, resulting in product recovery of 86% and purity of 92%. These results demonstrate that anion-exchange displacement chromatography can indeed be employed for large-scale oligonucleotide separations at high column loading.